Hamilton lapped the Autódromo Hermanos Rodríguez in one minute, 18.704 seconds, just over a quarter of a second quicker than Rosberg's last gasp lap, which put him the furthest up the order he has been all weekend..
Max Verstappen, who was fastest in the second part of qualifying with a time quicker than his Q3 effort, will start in third, alongside Red Bull team mate Daniel Ricciardo. Both drivers, along with Carlos Sainz, will be the only drivers in the top 10 to start the race on the supersoft tyre, with everyone else completing their Q2 laps on softs.
Nico Hulkenberg was a fine fifth for Force India, ahead of the Ferraris of Kimi Raikkonen and Sebastian Vettel who have slipped down the order after showing much promise during the early stages of the weekend.
Fernando Alonso will start 11th, a result he was thrilled with as it allows him a free choice of tyres for the start of tomorrow's race.
Sergio Perez was arguably the highest profile casualty of the second part of qualifying; the crowd favourite will start 12th, ahead of Jenson Button, Kevin Magnussen, Marcus Ericsson and Pascal Wehrlein.
The other Mexican in the field, Esteban Gutierrez, was the highest placed victim of Q1 - he will start 17th, with Daniil Kvyat, Felipe Nasr, Esteban Ocon and Romain Grosjean all also falling at the first hurdle.
Jolyon Palmer failed to take part in the session after he cracked his chassis in final practice. He will start from the pit lane.
Bahrain International Circuit - Winter testing